Compositions and methods for immunodominant antigens of Mycobacterium tuberculosis

ABSTRACT

Contemplated compositions, devices, and methods are drawn to various antigens from the pathogen  M. tuberculosis  and their use in vaccines, therapeutic agents, and various diagnostic tests. In particularly preferred aspects, the antigens are immunodominant and have quantified and known relative reactivities with respect to sera of a population infected with the pathogen, and/or have a known association with a disease parameter.

This application is a divisional application of allowed U.S. applicationSer. No. 13/681,224 filed Nov. 19, 2012, which is a divisionalapplication Ser. No. 13/396,213, filed Feb. 14, 2012, which is issued asU.S. Pat. No. 8,329,418, which is a divisional application of U.S.application Ser. No. 13/077,561, filed Mar. 31, 2011, which issued asU.S. Pat. No. 8,114,614, which is a divisional of U.S. application Ser.No. 12/465,136, filed May 13, 2009, which issued as U.S. Pat. No.7,927,818, which is continuation-in-part of our copending U.S.application Ser. No. 12/447,620 filed Dec. 3, 2009, which is a U.S.national phase filing of International Application No. PCT/US07/23299,which was filed Nov. 1, 2007 which claims priority to U.S. ProvisionalApplication No. 60/856,217, which was filed Nov. 1, 2006, all of whichare incorporated by reference herein in their entirety.

FIELD OF THE INVENTION

The field of the invention is compositions and methods related toselected antigens from Mycobacterium tuberculosis, especially as theyrelate to their use in diagnostic and therapeutic compositions andmethods.

BACKGROUND

Antigens for vaccination and/or diagnostic purposes are typically singleantigens from a pathogen, or complex mixtures of multiple known antigensfrom a pathogen, or of multiple known and unknown antigens of a pathogensuch as live, attenuated or inactivated bacteria or viruses. Dependingon the particular type of pathogen, single antigens may provide aquantifiable signal in immunodiagnostic tests (antibody or cellularresponses). However, due to variations among individuals in their immuneresponse profiles, single antigen tests are often not sufficient toobtain useful diagnostic information with useful specificity andsensitivity.

For example, multiple tests are often required for accurate diagnosis oftuberculosis (TB). Most typically, a person suspected of being infectedwith M. tuberculosis is tested using the tuberculin skin test (TST) thatoften provides variable results, which make their interpretation rarelyconsistent. Alternative tests are the interferon gamma release assays(IGRAs). These tests are more specific that TST but they still do notprovide means of distinguishing persons having active tuberculosis frompersons who are infected but are not currently harboring an activedisease process. For investigation of active TB, a sputum smear test foracid fast bacilli can be employed to identify M. tuberculosis directly,which tends to provide good specificity. However, the sensitivity varieswidely among different laboratories. To obtain a more definite result,active TB may be diagnosed by bacterial culture from, e.g., sputum orother bodily fluids. Unfortunately, such test requires a dedicatedmicrobiology laboratory and several weeks to obtain the results. Morerecently developed methods, such as real time PCR assays are relativelyaccurate but require sophisticated equipment and highly trainedpersonnel, and they are very susceptible to cross-sample contamination.

Based on the above drawbacks it is therefore desirable to develop anantibody-based test that would overcome at least some of thedifficulties associated with bacterial culture, genetic analysis orother known methods, and considerable effort has been spent defining andidentifying immunoreactive proteins in membrane fractions of M.tuberculosis and M. tuberculosis-conditioned culture medium (‘culturefiltrate proteins’ or CFPs). Candidate antigens are typically tested fordiagnostic utility in ELISAs and Western blots using TB sera and serafrom healthy controls. CFPs are more widely studied because of theconvenience of working with soluble proteins. Of the >100 M.tuberculosis proteins in culture filtrates (representing about 2.5% ofthe M. tuberculosis proteome), roughly two dozen are recognized by serafrom TB patients, most of which have been previously identified. Yetdespite these efforts, there remains no effective serological test withthe sensitivity and specificity required to accurately diagnose TB,particularly in the early stage of infection. Moreover, none of theheretofore known antigens is generally applicable to differentiate amongstages (e.g., active disease versus non-active), secondary infections,etc., as the signal is either impossible to deconvolute (e.g., compoundsignal from inactivated pathogen) or only provides a single data point.

Similarly, where known antigens are used in a vaccine, numerous problemsare known due to the variability of individual immune response andpotential prior exposure. More recently, multivalent vaccinepreparations have become available where in a single dose, multiple anddistinct antigens, from multiple and distinct serotypes, of a singlepathogenic organisms were combined (Prevnar™: Heptavalent vaccineagainst Streptococcus pneumoniae capsular serotypes 4, 6B, 9V, 14, 18C,19F, and 23F). While such mixed preparations tend to provide a broaderrange of protection against different serotypes, various difficultiesnevertheless remain. Most significantly, where a single antigen fails toelicit an immune response, coverage to the corresponding serotype is notpresent. Thus, combination of single defined antigens from severalserotypes merely combines benefits and problems associated with thesingle antigens.

Therefore, while numerous methods of identification and use of antigensare known in the art, all or almost all of them suffer from one or moredisadvantages. Consequently, there remains a large, unmet need toprovide improved compositions and methods of antigens from M.tuberculosis for diagnosis and therapy of TB.

SUMMARY OF THE INVENTION

The present invention is directed to immunodominant antigens from M.tuberculosis wherein the antigens are known to react, that is, haveknown reactivities (and particularly known relative reactivities) toserum of a population of patients infected with the pathogen. Thus, theantigens presented herein will have a statistically high probability toelicit an immune response in a relatively large group of patients.Further, where the antigens are determined from selected sub-populations(e.g., active stage, latent stage, past infection, prior vaccination,not infected, co-infection with other pathogen, etc.), the antigens mayalso have a known association with a disease parameter.

In aspect of the inventive subject matter, an antigen compositioncomprises a plurality of antigens of M. tuberculosis encoded by nucleicacids selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:586(or any subgroup of such sequences), or fragments thereof, wherein atleast two of the antigens elicit an immune response.

In other contemplated aspects of the inventive subject matter, anantigen composition comprises two or more immunodominant antigens of apathogenic organism and are associated with a carrier, wherein theantigens have quantified and known relative reactivities with respect tosera of a population infected with the organism, and wherein theantigens have a known association with a disease parameter. Mostpreferably, immunodominant antigens are polypeptides and are encoded bynucleic acids having a sequence according to SEQ ID NO:1 to SEQ IDNO:589 (or comprise fragments thereof).

It is further contemplated that the known reactivities may becharacterized by a variety of factors, however, it is particularlypreferred that the known reactivities are characterized by strength ofimmunogenicity and/or time course of the infection. It is generallypreferred that the parameter is activity state of the disease, aprevious exposure to the pathogen, the duration of exposure to thepathogen, a chronic infection, past disease, active infection, inactiveinfection, at least partial immunity to infection with the pathogen,and/or outcome upon treatment.

In another aspect of the inventive subject matter, the carrier is apharmaceutically acceptable carrier, and the composition is formulatedas a vaccine. In such aspects, it is generally preferred that thevaccine comprises multiple (e.g., at least two, four, or six) antigens.It is still further contemplated that the antigens or fragments thereofare at least partially purified and/or recombinant.

In further contemplated aspects, the carrier may also be a solidcarrier, and the plurality of antigens is disposed on the carrier eitheras a mixture or as an array. In such arrays, it is generally preferredthat the antigens have at least two distinct known reactivities and/orparameters. It is also contemplated that the antigens or fragmentsthereof may be in crude expression extracts, in partially purified form(e.g., purity of less than 60%), or in highly purified form (e.g.,purity of at least 95%). The antigens in such arrays may be recombinantor native. Alternatively, solid phases need not be limited to planararrays, but may also include beads, columns, dipstick-type formats, etc.

Aspects of this invention include diagnostic assay utilizing at leasttwo immunodominant antigens of M. tuberculosis. Antibody assays comprisecontacting a sample of bodily fluid that contains antibodies against M.tuberculosis, for example, serum, with at least two immunodominantantigens of this invention and detecting antigen-antibody binding by anysatisfactory method, preferably by formation of a color or generation ofa fluorescent signal. For example, antigens immobilized on a solidsurface, either individually in discrete areas or in a mixture, may beused to immobilize antibodies from the sample, and an anti-antibodylinked directly or indirectly to a color-forming enzyme may then beadded for signal generation in the standard ELISA format. Alternatively,fluorescence signals may be generated by methods such as linking(directly or indirectly) an anti-antibody to a fluorescence-emittingsubstance. Aspects of this invention also include use of at least twoimmunodominant antigens free in solution rather than immobilized on asurface. For example, a sample of peripheral blood, a bodily fluidcontaining T-lymphocytes, may be contacted with such antigens in vitro.Reactions between T-lymphocytes and antigen (on an antigen-presentingcell) are, like antigen-antibody reactions, epitope-specific even thoughT-lymphocytes and antibodies may recognize different epitopes. If theantigens are recognized, the T-lymphocytes produce at least onecytokine, such as interferon gamma, which is then detected by a(directly or indirectly) labeled antibody. Aspects of this inventionfurther include kits of reagents for performing assays. Such kitsinclude at least two immunodominant antigens according to thisinvention.

Various objects, features, aspects and advantages of the inventivesubject matter will become more apparent from the following detaileddescription of preferred embodiments, along with the accompanyingdrawing figures in which like numerals represent like components.

BRIEF DESCRIPTION OF THE DRAWING

FIGS. 1A and 1B depict exemplary microarrays probed with sera fromTB-positive and LTBI-negative (i.e., not infected with M. tuberculosis)individuals, respectively.

FIGS. 2A and 2B are graphs depicting exemplary statisticalrepresentations in differences in signals for TB-positive andLTBI-negative results.

FIG. 2C is a table listing selected TB antigens using one preferredexemplary ranking algorithm.

FIGS. 3A and 3B depict exemplary fluorimetric and colorimetricvisualization of exemplary microarrays and respective scatter plotsindicating the correlation between the visualizations.

FIGS. 4A and 4B depict the proteins ranking in random forests, CERNO,and random forests with CERNO-prefiltered data.

FIG. 5 depicts a protein which exhibits a tail distribution of higherintensity signals in TB samples that is not seen in non-TB samples.

DETAILED DESCRIPTION

The inventors have discovered various immunodominant antigens from M.tuberculosis that are suitable for diagnostic and therapeutic purposes.Particularly preferred immunodominant antigens and are those encoded bynucleic acids having a sequence according to SEQ ID NO:1 to SEQ IDNO:586, and it is generally contemplated that such antigens can be usedas single antigens, or in combination (optionally also in combinationwith antigens from another pathogen) in the manufacture of variousdiagnostic devices, therapeutic compositions, and vaccines. Preferably,the immunodominant antigens suitable for diagnostic and therapeuticpurposes are encoded by the sequences designated Rv0798c (SEQ IDNO:121), Rv1886c (SEQ ID NO:270), Rv2031c (SEQ ID NO:284), Rv3616c (SEQID NO:509), Rv3804c (SEQ ID NO:534), Rv3874 (SEQ ID NO:547), Rv0302 (SEQID NO:52), Rv0379 (SEQ ID NO:65), Rv0394c (SEQ ID NO:66), Rv0456c (SEQID NO:74), Rv0632c (SEQ ID NO:103), Rv0944 (SEQ ID NO:142), Rv0984 (SEQID NO:146), Rv1030 (SEQ ID NO:153), Rv1196 (SEQ ID NO:174), Rv1242 (SEQID NO:180), Rv1284 (SEQ ID NO:187), Rv1387 (SEQ ID NO:206), Rv1837c (SEQID NO:264), Rv1926c (SEQ ID NO:275), Rv1980c (SEQ ID NO:281), Rv2094c(SEQ ID NO:294), Rv2544 (SEQ ID NO:363), Rv2618 (SEQ ID NO:375), Rv2746c(SEQ ID NO:391), Rv2870c (SEQ ID NO:407), Rv2873 (SEQ ID NO:408), Rv2875(SEQ ID NO:409), Rv3050c (SEQ ID NO:434), Rv3248c (SEQ ID NO:458),Rv3376 (SEQ ID NO:478), Rv3763 (SEQ ID NO:527), Rv3810 (SEQ ID NO:536),Rv3864 (SEQ ID NO:545), Rv2252 (SEQ ID NO:323), Rv2282c (SEQ ID NO:569),Rv0212c (SEQ ID NO:557), Rv3243c (SEQ ID NO:456), Rv3675 (SEQ IDNO:519), Rv2984 (SEQ ID NO:423), Rv1175c (SEQ ID NO:169), Rv3326 (SEQ IDNO:578), Rv3628 (SEQ ID NO:513), Rv3775 (SEQ ID NO:584), Rv3362c (SEQ IDNO:475), Rv0801 (SEQ ID NO:122), Rv1629 (SEQ ID NO:566), Rv0272c (SEQ IDNO:558), Rv3762c (SEQ ID NO:583), Rv3319 (SEQ ID NO:577), Rv3495c (SEQID NO:581), Rv2151c (SEQ ID NO:308), Rv0227c (SEQ ID NO:37), Rv0280 (SEQID NO:50), Rv0993 (SEQ ID NO:148), Rv1306 (SEQ ID NO:192), Rv1363c (SEQID NO:204), Rv2050 (SEQ ID NO:288), Rv2116 (SEQ ID NO:299), Rv3417c (SEQID NO:486), Rv3653 (SEQ ID NO:516), Rv1253 (SEQ ID NO:182), Rv3413c (SEQID NO:485), Rv1635c (SEQ ID NO:232), Rv3021c (SEQ ID NO:432), Rv1193(SEQ ID NO:173), Rv2592c (SEQ ID NO:369), Rv3620c (SEQ ID NO:510),Rv0929 (SEQ ID NO:139), Rv0959 (SEQ ID NO:145), Rv1162 (SEQ ID NO:166),Rv2389c (SEQ ID NO:341), Rv2984 (SEQ ID NO:423), Rv2588c (SEQ IDNO:367), Rv0171 (SEQ ID NO:26), Rv1865c (SEQ ID NO:267), Rv2074 (SEQ IDNO:290), Rv0543c (SEQ ID NO:87), Rv1677 (SEQ ID NO:237), Rv1304 (SEQ IDNO:191), Rv2841c (SEQ ID NO:400), Rv3680 (SEQ ID NO:520), Rv0831c (SEQID NO:125), Rv2032 (SEQ ID NO:285), Rv3127 (SEQ ID NO:446), Rv3272 (SEQID NO:464), Rv3323c (SEQ ID NO:470), Rv3508 (SEQ ID NO:494), Rv3628 (SEQID NO:513), Rv1173 (SEQ ID NO:167), Rv2623 (SEQ ID NO:376), Rv0527 (SEQID NO:85), Rv1620c (SEQ ID NO:229), Rv1901 (SEQ ID NO:272), Rv2151c (SEQID NO:308), Rv0362 (SEQ ID NO:60), Rv3129 (SEQ ID NO:447), Rv3140 (SEQID NO:449), Rv0340 (SEQ ID NO:56), Rv2792c (SEQ ID NO:395), Rv3003c (SEQID NO:426), Rv3019c (SEQ ID NO:431), Rv3862c (SEQ ID NO:544), Rv0572c(SEQ ID NO:91), Rv2477c (SEQ ID NO:356), Rv2659c (SEQ ID NO:379), Rv0311(SEQ ID NO:54), Rv0350 (SEQ ID NO:57), Rv2127 (SEQ ID NO:301), Rv3875(SEQ ID NO:548), Rv0877 (SEQ ID NO:134), Rv1916 (SEQ ID NO:274), Rv2138(SEQ ID NO:303), Rv2847c (SEQ ID NO:403), Rv3118 (SEQ ID NO:444),Rv2495c (SEQ ID NO:358), Rv3669 (SEQ ID NO:517), Rv0281 (SEQ ID NO:51),Rv2711 (SEQ ID NO:383), Rv2744c (SEQ ID NO:390), Rv3803c (SEQ IDNO:533), Rv1239c (SEQ ID NO:179), Rv2147c (SEQ ID NO:307), Rv2253 (SEQID NO:324), Rv0308 (SEQ ID NO:53), Rv0587 (SEQ ID NO:95), Rv1564c (SEQID NO:224), Rv2185c (SEQ ID NO:313), Rv1805c (SEQ ID NO:261), Rv2729c(SEQ ID NO:386), Rv3386 (SEQ ID NO:481), Rv3515c (SEQ ID NO:497), Rv0772(SEQ ID NO:116), Rv2948c (SEQ ID NO:420), Rv0006 (SEQ ID NO:1), Rv1906c(SEQ ID NO:273), Rv2244 (SEQ ID NO:322), Rv2468c (SEQ ID NO:354),Rv3701c (SEQ ID NO:522), Rv0054 (SEQ ID NO:6), Rv1945 (SEQ ID NO:277),Rv3345c (SEQ ID NO:472), Rv0276 (SEQ ID NO:48), Rv0709 (SEQ ID NO:108),Rv1527c (SEQ ID NO:220), Rv2048c (SEQ ID NO:287), Rv2414c (SEQ IDNO:345), Rv3524 (SEQ ID NO:499), Rv3556c (SEQ ID NO:502), Rv1322 (SEQ IDNO:196), Rv2934 (SEQ ID NO:417), Rv0270 (SEQ ID NO:47), Rv0612 (SEQ IDNO:99), Rv1699 (SEQ ID NO:242), Rv2728c (SEQ ID NO:385), Rv3017c (SEQ IDNO:430), Rv3364c (SEQ ID NO:476), Rv3418c (SEQ ID NO:487), Rv3718c (SEQID NO:525), Rv0426c (SEQ ID NO:70), Rv1181 (SEQ ID NO:171), Rv1725c (SEQID NO:250), Rv0256c (SEQ ID NO:44), Rv0605 (SEQ ID NO:98), Rv0737 (SEQID NO:114), Rv0834c (SEQ ID NO:126), Rv1255c (SEQ ID NO:184), Rv2224c(SEQ ID NO:320), Rv1843c (SEQ ID NO:265), Rv2333c (SEQ ID NO:334),Rv2490c (SEQ ID NO:357), Rv3183 (SEQ ID NO:454), Rv0668 (SEQ ID NO:106),Rv1556 (SEQ ID NO:223), Rv1673c (SEQ ID NO:236), Rv3513c (SEQ IDNO:496), Rv3675 (SEQ ID NO:519), Rv3870 (SEQ ID NO:546), Rv3891c (SEQ IDNO:552), Rv0163 (SEQ ID NO:24), Rv0710 (SEQ ID NO:109), Rv1297 (SEQ IDNO:189), Rv1745c (SEQ ID NO:255), Rv0600c (SEQ ID NO:97), Rv1536 (SEQ IDNO:222), Rv1738 (SEQ ID NO:254), Rv2524c (SEQ ID NO:359), Rv3086 (SEQ IDNO:440), Rv3367 (SEQ ID NO:477), Rv0135c (SEQ ID NO:20), Rv0627 (SEQ IDNO:101), Rv1448c (SEQ ID NO:213), Rv3224a (SEQ ID NO:455), Rv0029 (SEQID NO:2), Rv0846c (SEQ ID NO:129), Rv1159 (SEQ ID NO:165), Rv1186c (SEQID NO:172), Rv1705c (SEQ ID NO:243), Rv1713 (SEQ ID NO:248), Rv2476c(SEQ ID NO:355), Rv3402c (SEQ ID NO:483), Rv2615c (SEQ ID NO:374),Rv2995c (SEQ ID NO:425), Rv3788 (SEQ ID NO:585), Rv0140 (SEQ ID NO:555),Rv0203 (SEQ ID NO:33), Rv1531 (SEQ ID NO:565), Rv1693 (SEQ ID NO:241),Rv1882c (SEQ ID NO:269), Rv2143 (SEQ ID NO:568), Rv2367c (SEQ IDNO:570), Rv0584 (SEQ ID NO:94), Rv1651c (SEQ ID NO:567), Rv3197a (SEQ IDNO:576), Rv3369 (SEQ ID NO:579), Rv3825c (SEQ ID NO:586), Rv0101 (SEQ IDNO:15), Rv0808 (SEQ ID NO:123), Rv0814c (SEQ ID NO:560), Rv2153c (SEQ IDNO:309), Rv2933 (SEQ ID NO:416), Rv0071 (SEQ ID NO:9), Rv2471 (SEQ IDNO:571), Rv2979c (SEQ ID NO:575), Rv0155 (SEQ ID NO:556), Rv0581 (SEQ IDNO:559), Rv2631 (SEQ ID NO:377), Rv3455c (SEQ ID NO:489), Rv3601c (SEQID NO:505), Rv0896 (SEQ ID NO:562), Rv1641 (SEQ ID NO:234), Rv3005c (SEQID NO:427), Rv3759c (SEQ ID NO:582), Rv3800c (SEQ ID NO:532), Rv0187(SEQ ID NO:30), Rv2379c (SEQ ID NO:338), Rv2434c (SEQ ID NO:352),Rv2940c (SEQ ID NO:574), Rv3477 (SEQ ID NO:580), Rv0435c (SEQ ID NO:72),Rv0844c (SEQ ID NO:128), Rv0856 (SEQ ID NO:561), Rv1191 (SEQ ID NO:564),Rv2803 (SEQ ID NO:397), Rv0783c (SEQ ID NO:118), Rv1054 (SEQ ID NO:563),Rv1689 (SEQ ID NO:240), Rv2539c (SEQ ID NO:572), Rv2859c (SEQ IDNO:573), Rv3777 (SEQ ID NO:528), and fragments thereof. Most preferably,the immunodominant antigens are encoded by sequences designated Rv0798c(SEQ ID NO:121); Rv1886c (SEQ ID NO:270); Rv2031c (SEQ ID NO:284);Rv3616c (SEQ ID NO:509); Rv3804c (SEQ ID NO:534); and Rv3874 (SEQ IDNO:547).

As used herein, the term “immunodominant antigen” refers to an antigenthat elicits in at least one stage of the infection production of one ormore types of antibodies (e.g., IgG, IgA, IgE, IgM, etc.) in at least20%, more typically at least 40%, and most typically at least 70% of apopulation exposed to the antigen, or wherein, when compared to otherantigens of the same pathogen, the average binding affinity and/oraverage quantity of the antibodies produced in the patient in at leastone stage of the disease is at least in the upper half, more typicallyupper tertile, and most typically upper quartile. Most typically, theaverage binding affinity and/or average quantity of the antibodies isreflected in the signal intensity and signal intensity can therefore beused as a surrogate marker for average binding affinity and/or averagequantity of the antibodies. In further aspects, preferred immunodominantantigens are also characterized by a response in the test group that isconsidered statistically significant when compared with control signalintensity, wherein the significance level p is preferably equal or lessthan 0.1, more preferably equal or less than 0.05, and most preferablyequal or less than 0.01.

In one aspect of the inventive subject matter, immunodominant antigensare identified from a proteome screen against sera of a population thathas been previously exposed to the pathogen. Most preferably, thepopulation is subdivided in several sub-populations to reflect variousdisease parameters (e.g., active disease, bacillary burden of disease,latent infection, presence of co-infection with HIV, absence ofinfection, etc.), which can then be correlated with antibody responsesto the so identified antigens. It is still further preferred that thescreening also provides data on relative reactivities with respect tothe antigens and sera of the populations/sub-populations.

It is generally preferred that at least part of the pathogen's genome isobtained and all potential open reading frames and portions thereof aredetermined in silico. Once the potential genes are identified, suitableprimers are determined to provide amplicons of the entire Open ReadingFrames (ORFs), or, less preferably, portions thereof, wherein theprimers are preferably designed to allow facile subcloning into anexpression system. Most preferably, the subcloning usesrecombinase-based subcloning using unpurified PCR mixtures to avoidcloning bias, and the so obtained recombinant plasmids are polyclonallymultiplied, which enables unbiased presentation of the amplicons. It isstill further particularly preferred that the plasmid preparations arethen subjected to an in vitro transcription/translation reaction tothereby provide the recombinant ORF peptide, which is then spotted orotherwise immobilized onto a suitable addressable carrier (e.g.,membrane, bead, etc.).

It should be recognized that the so prepared proteomes can then beexposed to serum of a population of control individuals and/orpopulation of individuals that are known to have current or previousexposure to the above pathogen from which the ORFs were prepared.Antibodies of the serum that bind to one or more of the ORFs are thendetected using well known methods (e.g., use of secondary antibodies).In this manner, the entire proteome of the pathogen can be rapidlyassessed for immunogenicity and potential binding with antibodies inserum. Various preferred aspects, compositions, and methods of proteomepreparation are disclosed in International patent publication number WO06/088492, which is incorporated by reference herein.

Therefore, and among various other advantages, it should be especiallyrecognized that contemplated compositions and methods presented hereinwill allow for preparation of vaccines and diagnostic compositionscomprising a plurality of antigens with known and predetermined affinityto target ORFs of a pathogen. As individual immune systems are known toexhibit significant variation with respect to antigen recognition,methods and compositions contemplated herein will allow statisticallysupported antigen identification to identify immunodominant antigens ina population of patient. Consequently, multiple targets can be used toelicit an immune response and/or detect a prior exposure, even where oneor more of the targets may be evasive for detection or provide only aweak response.

With respect to the immunodominant sequences identified herein, itshould be further appreciated that the sequences need not be completeORFs, but that suitable sequences may also be partial sequences (e.g.,synthetic, recombinant or isolated) that typically comprise at leastpart of an antigenic epitope. For example, contemplated DNA sequencesinclude those that will hybridize under stringent hybridizationconditions to respective sequences listed in the sequence listing. Thus,sequences contemplated herein may be identified as DNA sequencesencoding the antigenic peptide (partial or entire ORF), or may beidentified as peptide sequence (or homologs thereof). Similarly,chemically modified antigens, and/or orthologs of the polypeptidespresented herein are also deemed suitable for use herein.

It should be particularly noted that while proteome screening willprovide a plurality of antigens as potentially useful molecules fordiagnosis, vaccination, and/or therapy, such an approach only provides araw cut of (a plurality) of individual responses. Therefore, as mostindividual immune reactions towards the same pathogen elicit asignificantly distinct profile of antibodies (e.g., depending on diseasestage, previous exposure, and/or inter-individual variability), resultsobtained from such screening are typically inhomogeneous. Consequently,variability of the individual immune responses and variability of thequantity of recombinant protein in the array must be taken intoconsideration to obtain meaningful results.

Therefore, it should be appreciated that filtering of raw data willresult in a collection of antigens with quantified and known relativereactivities with respect to sera of a population infected with thepathogen. Moreover, it should be noted that as signals may be specificto a particular stage in the course of an infection, relativereactivities may be indicative of the time course of the infection,and/or relative reactivities may represent differences in the strengthof immunogenicity of the particular antigen (or quantity of depositedantigen in the screening assay). Additionally, it should be particularlyrecognized that depending on the choice of the specific patientpopulation, the tested sera will reflect the immune status of apopulation that is characterized by one or more parameters of thedisease. For example, populations may be observed that are infected ornot infected, that had a long-term exposure or chronic infection, thathad spontaneous recovery, that represents a group of responders (ornon-responders) to a particular drug treatment, or that had at leastpartial immunity to the pathogen.

In still further contemplated aspects, immunodominant antigens areidentified by selecting for an antigen (preferably within a well-definedsub-population) that (a) produces in at least 40-50% of a population ameasurable signal, and (b) has a signal strength of at least 40% of theoverall average signal intensity. However, and more preferably, thesignal strength will be at least above average of the overall averagesignal intensity, and even more preferably in the upper tertile(quartile, or even quintile) of signal intensities in the assay.Therefore, and viewed from another perspective, immunodominant antigenswill preferably be selected in a comparison of at least two series oftests, wherein one series of tests is typically the sub-population(e.g., primary infection, active disease, latent infection, recovering,previously diseased, chronic, etc.) and the other series of tests is thecontrol group (e.g., other sub-population or control group). Stillfurther, it is generally preferred that the series of tests also includea negative control against which the potential immunodominant antigensare compared.

Consequently, and with particular respect to the pathogen presentedherein, it should be appreciated that compositions comprising one ormore selected immunodominant antigens can be prepared that will have astatistically high probability to elicit or have elicited an immuneresponse in a relatively large group of patients. Further, where theantigens are determined from selected sub-populations (e.g., activedisease, severity of disease, latent infection, previously diseasedpatients, primary infection, etc.), the antigens also have a knownassociation with a disease parameter and thus allow staging of thedisease and/or prediction of therapeutic efficacy. Moreover, as theantigens presented herein are immunodominant antigens, it should benoted that vaccine compositions can be prepared with known orpredictable immunogenicity.

More specifically, antigens from M. tuberculosis encoded by the nucleicacids of SEQ ID NO:1 to SEQ ID NO:586 were identified as immunodominant(see examples below). With respect to the reading frame for each of thesequences of SEQ ID NO:1 to SEQ ID NO:586, it should be noted that thefirst base in the sequences is either the first base of the start codonor the first base in the first codon of the polypeptide that wasidentified with the methods and compositions provided herein. Mosttypically, the last three bases denote the stop codon, or the last baseof the last codon of the polypeptide that was identified with themethods and compositions provided herein.

In these examples, each of the antigens was characterized, inter alia,with regard to their individual and relative reactivities for thepathogen. Most typically, reactivity was measured as strength ofimmunogenicity (e.g., such that average binding affinity and/or averagequantity of the antibodies produced a predetermined signal intensity(e.g., in the upper half, upper tertile, or even upper quartile)).Viewed from a different perspective, each one of the identified antigenshas a known signal strength (reflecting the quantity of antibodiesformed in the patient) in the assay as described below relative toanother one of the identified antigens. Some proteins, such as the onedepicted in FIG. 5, exhibit a tail distribution of higher intensitysignals in TB samples that is not seen in non-TB samples. These twoviolin plots show the distribution of log 10-transformed signalintensities measured for a representative protein in sera from TB casesvs. sera from non-TB disease cases. Proteins having this characteristicdistribution were identified on the examples described below byimplementing a calculation whereby the null hypothesis could be rejectedthat the profile of a sample comprised only reactivity values consistentwith the non-TB intensity distribution.

Furthermore, each of the identified antigens was also characterized byassociation with at least one parameter. In most cases, the diseaseparameter was active disease after infection, and in further cases, thedisease parameter was number of tubercle bacilli in sputum orradiographic extent of disease, and in further cases, history of pastdisease in the non-diseased population. Therefore, it should beespecially appreciated that identification of immunodominant antigenswill not only allow for identification of statistically meaningfulantigens for diagnosis, vaccine development, and treatment, but alsoallow to develop a stage specific tool to identify candidate moleculesto fine-tune diagnosis and/or treatment.

For example, suitable diagnostic devices especially include thosecomprising one or more of the immunodominant antigens, fragments, oranalogs thereof that are encoded by nucleic acids according to SEQ IDNO:1 to SEQ ID NO: 589, preferably Rv0798c (SEQ ID NO:121), Rv1886c (SEQID NO:270), Rv2031c (SEQ ID NO:284), Rv3616c (SEQ ID NO:509), Rv3804c(SEQ ID NO:534), Rv3874 (SEQ ID NO:547), Rv0302 (SEQ ID NO:52), Rv0379(SEQ ID NO:65), Rv0394c (SEQ ID NO:66), Rv0456c (SEQ ID NO:74), Rv0632c(SEQ ID NO:103), Rv0944 (SEQ ID NO:142), Rv0984 (SEQ ID NO:146), Rv1030(SEQ ID NO:153), Rv1196 (SEQ ID NO:174), Rv1242 (SEQ ID NO:180), Rv1284(SEQ ID NO:187), Rv1387 (SEQ ID NO:206), Rv1837c (SEQ ID NO:264),Rv1926c (SEQ ID NO:275), Rv1980c (SEQ ID NO:281), Rv2094c (SEQ IDNO:294), Rv2544 (SEQ ID NO:363), Rv2618 (SEQ ID NO:375), Rv2746c (SEQ IDNO:391), Rv2870c (SEQ ID NO:407), Rv2873 (SEQ ID NO:408), Rv2875 (SEQ IDNO:409), Rv3050c (SEQ ID NO:434), Rv3248c (SEQ ID NO:458), Rv3376 (SEQID NO:478), Rv3763 (SEQ ID NO:527), Rv3810 (SEQ ID NO:536), Rv3864 (SEQID NO:545), Rv2252 (SEQ ID NO:323), Rv2282c (SEQ ID NO:569), Rv0212c(SEQ ID NO:557), Rv3243c (SEQ ID NO:456), Rv3675 (SEQ ID NO:519), Rv2984(SEQ ID NO:423), Rv1175c (SEQ ID NO:169), Rv3326 (SEQ ID NO:578), Rv3628(SEQ ID NO:513), Rv3775 (SEQ ID NO:584), Rv3362c (SEQ ID NO:475), Rv0801(SEQ ID NO:122), Rv1629 (SEQ ID NO:566), Rv0272c (SEQ ID NO:558),Rv3762c (SEQ ID NO:583), Rv3319 (SEQ ID NO:577), Rv3495c (SEQ IDNO:581), Rv2151c (SEQ ID NO:308), Rv0227c (SEQ ID NO:37), Rv0280 (SEQ IDNO:50), Rv0993 (SEQ ID NO:148), Rv1306 (SEQ ID NO:192), Rv1363c (SEQ IDNO:204), Rv2050 (SEQ ID NO:288), Rv2116 (SEQ ID NO:299), Rv3417c (SEQ IDNO:486), Rv3653 (SEQ ID NO:516), Rv1253 (SEQ ID NO:182), Rv3413c (SEQ IDNO:485), Rv1635c (SEQ ID NO:232), Rv3021c (SEQ ID NO:432), Rv1193 (SEQID NO:173), Rv2592c (SEQ ID NO:369), Rv3620c (SEQ ID NO:510), Rv0929(SEQ ID NO:139), Rv0959 (SEQ ID NO:145), Rv1162 (SEQ ID NO:166), Rv2389c(SEQ ID NO:341), Rv2984 (SEQ ID NO:423), Rv2588c (SEQ ID NO:367), Rv0171(SEQ ID NO:26), Rv1865c (SEQ ID NO:267), Rv2074 (SEQ ID NO:290), Rv0543c(SEQ ID NO:87), Rv1677 (SEQ ID NO:237), Rv1304 (SEQ ID NO:191), Rv2841c(SEQ ID NO:400), Rv3680 (SEQ ID NO:520), Rv0831c (SEQ ID NO:125), Rv2032(SEQ ID NO:285), Rv3127 (SEQ ID NO:446), Rv3272 (SEQ ID NO:464), Rv3323c(SEQ ID NO:470), Rv3508 (SEQ ID NO:494), Rv3628 (SEQ ID NO:513), Rv1173(SEQ ID NO:167), Rv2623 (SEQ ID NO:376), Rv0527 (SEQ ID NO:85), Rv1620c(SEQ ID NO:229), Rv1901 (SEQ ID NO:272), Rv2151c (SEQ ID NO:308), Rv0362(SEQ ID NO:60), Rv3129 (SEQ ID NO:447), Rv3140 (SEQ ID NO:449), Rv0340(SEQ ID NO:56), Rv2792c (SEQ ID NO:395), Rv3003c (SEQ ID NO:426),Rv3019c (SEQ ID NO:431), Rv3862c (SEQ ID NO:544), Rv0572c (SEQ IDNO:91), Rv2477c (SEQ ID NO:356), Rv2659c (SEQ ID NO:379), Rv0311 (SEQ IDNO:54), Rv0350 (SEQ ID NO:57), Rv2127 (SEQ ID NO:301), Rv3875 (SEQ IDNO:548), Rv0877 (SEQ ID NO:134), Rv1916 (SEQ ID NO:274), Rv2138 (SEQ IDNO:303), Rv2847c (SEQ ID NO:403), Rv3118 (SEQ ID NO:444), Rv2495c (SEQID NO:358), Rv3669 (SEQ ID NO:517), Rv0281 (SEQ ID NO:51), Rv2711 (SEQID NO:383), Rv2744c (SEQ ID NO:390), Rv3803c (SEQ ID NO:533), Rv1239c(SEQ ID NO:179), Rv2147c (SEQ ID NO:307), Rv2253 (SEQ ID NO:324), Rv0308(SEQ ID NO:53), Rv0587 (SEQ ID NO:95), Rv1564c (SEQ ID NO:224), Rv2185c(SEQ ID NO:313), Rv1805c (SEQ ID NO:261), Rv2729c (SEQ ID NO:386),Rv3386 (SEQ ID NO:481), Rv3515c (SEQ ID NO:497), Rv0772 (SEQ ID NO:116),Rv2948c (SEQ ID NO:420), Rv0006 (SEQ ID NO:1), Rv1906c (SEQ ID NO:273),Rv2244 (SEQ ID NO:322), Rv2468c (SEQ ID NO:354), Rv3701c (SEQ IDNO:522), Rv0054 (SEQ ID NO:6), Rv1945 (SEQ ID NO:277), Rv3345c (SEQ IDNO:472), Rv0276 (SEQ ID NO:48), Rv0709 (SEQ ID NO:108), Rv1527c (SEQ IDNO:220), Rv2048c (SEQ ID NO:287), Rv2414c (SEQ ID NO:345), Rv3524 (SEQID NO:499), Rv3556c (SEQ ID NO:502), Rv1322 (SEQ ID NO:196), Rv2934 (SEQID NO:417), Rv0270 (SEQ ID NO:47), Rv0612 (SEQ ID NO:99), Rv1699 (SEQ IDNO:242), Rv2728c (SEQ ID NO:385), Rv3017c (SEQ ID NO:430), Rv3364c (SEQID NO:476), Rv3418c (SEQ ID NO:487), Rv3718c (SEQ ID NO:525), Rv0426c(SEQ ID NO:70), Rv1181 (SEQ ID NO:171), Rv1725c (SEQ ID NO:250), Rv0256c(SEQ ID NO:44), Rv0605 (SEQ ID NO:98), Rv0737 (SEQ ID NO:114), Rv0834c(SEQ ID NO:126), Rv1255c (SEQ ID NO:184), Rv2224c (SEQ ID NO:320),Rv1843c (SEQ ID NO:265), Rv2333c (SEQ ID NO:334), Rv2490c (SEQ IDNO:357), Rv3183 (SEQ ID NO:454), Rv0668 (SEQ ID NO:106), Rv1556 (SEQ IDNO:223), Rv1673c (SEQ ID NO:236), Rv3513c (SEQ ID NO:496), Rv3675 (SEQID NO:519), Rv3870 (SEQ ID NO:546), Rv3891c (SEQ ID NO:552), Rv0163 (SEQID NO:24), Rv0710 (SEQ ID NO:109), Rv1297 (SEQ ID NO:189), Rv1745c (SEQID NO:255), Rv0600c (SEQ ID NO:97), Rv1536 (SEQ ID NO:222), Rv1738 (SEQID NO:254), Rv2524c (SEQ ID NO:359), Rv3086 (SEQ ID NO:440), Rv3367 (SEQID NO:477), Rv0135c (SEQ ID NO:20), Rv0627 (SEQ ID NO:101), Rv1448c (SEQID NO:213), Rv3224a (SEQ ID NO:455), Rv0029 (SEQ ID NO:2), Rv0846c (SEQID NO:129), Rv1159 (SEQ ID NO:165), Rv1186c (SEQ ID NO:172), Rv1705c(SEQ ID NO:243), Rv1713 (SEQ ID NO:248), Rv2476c (SEQ ID NO:355),Rv3402c (SEQ ID NO:483), Rv2615c (SEQ ID NO:374), Rv2995c (SEQ IDNO:425), Rv3788 (SEQ ID NO:585), Rv0140 (SEQ ID NO:555), Rv0203 (SEQ IDNO:33), Rv1531 (SEQ ID NO:565), Rv1693 (SEQ ID NO:241), Rv1882c (SEQ IDNO:269), Rv2143 (SEQ ID NO:568), Rv2367c (SEQ ID NO:570), Rv0584 (SEQ IDNO:94), Rv1651c (SEQ ID NO:567), Rv3197a (SEQ ID NO:576), Rv3369 (SEQ IDNO:579), Rv3825c (SEQ ID NO:586), Rv0101 (SEQ ID NO:15), Rv0808 (SEQ IDNO:123), Rv0814c (SEQ ID NO:560), Rv2153c (SEQ ID NO:309), Rv2933 (SEQID NO:416), Rv0071 (SEQ ID NO:9), Rv2471 (SEQ ID NO:571), Rv2979c (SEQID NO:575), Rv0155 (SEQ ID NO:556), Rv0581 (SEQ ID NO:559), Rv2631 (SEQID NO:377), Rv3455c (SEQ ID NO:489), Rv3601c (SEQ ID NO:505), Rv0896(SEQ ID NO:562), Rv1641 (SEQ ID NO:234), Rv3005c (SEQ ID NO:427),Rv3759c (SEQ ID NO:582), Rv3800c (SEQ ID NO:532), Rv0187 (SEQ ID NO:30),Rv2379c (SEQ ID NO:338), Rv2434c (SEQ ID NO:352), Rv2940c (SEQ IDNO:574), Rv3477 (SEQ ID NO:580), Rv0435c (SEQ ID NO:72), Rv0844c (SEQ IDNO:128), Rv0856 (SEQ ID NO:561), Rv1191 (SEQ ID NO:564), Rv2803 (SEQ IDNO:397), Rv0783c (SEQ ID NO:118), Rv1054 (SEQ ID NO:563), Rv1689 (SEQ IDNO:240), Rv2539c (SEQ ID NO:572), Rv2859c (SEQ ID NO:573), Rv3777 (SEQID NO:528).

Depending on the particular device format, the device may have only asingle immunodominant antigen, fragment, or analog that may be used fordetection of binding of antibodies from blood, plasma or serum or otherbodily fluids containing antibody in an automated manner or by visualobservation. For example, where a single immunodominant antigen isemployed, suitable devices may be in the format of a dipstick orcompetitive ELISA. On the other hand, where multiple immunodominantantigens are employed, suitable devices may be in the format of an arraythat can be read in an automated device (e.g., via scanner) or visualmanner (e.g., dye-forming colorimetric reaction). Most typically, insuch devices, the plurality of antigens is deposited in a spatiallyaddressable manner (e.g., x-y matrix or beads with color association ormicrotiter plate). Moreover, it should be noted that diagnostic devicescontemplated herein may be based on numerous well known manners ofdetection, including ELISA (sandwich or non-sandwich), competitiveELISA, anti-idiotypic antibodies, etc., wherein all known colorimetricand photometric (e.g., fluorescence, luminescence, etc.) or radiometricreactions are deemed suitable for use.

In most typical devices, a plurality of immunodominant antigens of asingle (or multiple) pathogen and/or serotype are deposited on a solidsurface or onto an addressable solid phase and exposed to blood, serum,plasma or other antibody-containing body fluid. Consequently, soprepared compositions can be employed to identify and/or characterize animmune response of an individual against selected antigens, andoptionally assess the kind of immune response (e.g., identification oflatent or chronic infection), as well as disease progression, efficacyof therapy, etc. Most typically, the plurality of antigens will includebetween 5 to 10 antigens, but significantly higher amounts of antigensare also contemplated, including at least 25%, more typically at least50%, even more typically at least 75%, and most typically at least 90%of the proteome of the pathogen. Similarly, less than 5 antigens (1-4)are also deemed suitable. In further typical aspects of the inventivesubject matter, contemplated arrays are most preferably processed in amicrofluidic device. For example, an array of antigens in such devicesmay be printed on a membrane or other material (e.g.,nitrocellulose-coated carrier of less than 1 cm2 area) that is thenplaced in a microfluidic device having sample/reagent inlet and outletports. Depending on the specific configuration, signals may be acquiredusing optical methods (e.g., CCD chip, flat bed scanner, etc.),electrical methods (e.g., voltametric or amperometric), or other methodswell known in the art. Alternatively, visual detection or detectionusing a regular flat bed scanner at 1200 dpi resolution and/orfluorescence detection is also deemed suitable.

In another example, immunodominant antigens according to the inventivesubject matter may also be employed to generate an antibody preparationthat can be used as passive vaccination for therapeutic treatment oftuberculosis. In preferred embodiments, such vaccines are subunitvaccines or attenuated live recombinant vaccines. For example, theimmunodominant antigens presented herein may be employed in themanufacture of a vaccine that comprises at least one, and more typicallyat least two of the immunodominant antigens encoded by nucleic acidsaccording to SEQ ID NO:1 to SEQ ID NO:586. More preferably, however,contemplated vaccines will include between two and five, or at leastsix, and even more antigens, of which at least one of the antigens is animmunodominant antigen. Such vaccine compositions may be directed toelicit immunity against single or multiple subtypes and may thuscomprise distinct immunodominant antigens, optionally from multiple anddistinct subtypes. Moreover, it should be appreciated that vaccines maybe produced that predominantly, or even exclusively, compriseimmunodominant antigens of a single parameter. For example, a vaccinemay comprise immunodominant antigens that are characteristic for apopulation that has a latent infection. In less preferred aspects, thesequences according to SEQ ID NO:1 to SEQ ID NO:586 may also be employedas DNA vaccines, or be part of an in vivo expression system thattriggers an immune response against the in vivo produced recombinantantigen or fragment thereof.

Additionally, it is contemplated that antigens identified herein mayalso be employed to generate (monoclonal or polyclonal) antibodies orfragments thereof (e.g., Fab, scFv, etc.) that can then be employed in adiagnostic test that directly detects the presence of the antigen inblood, blood derivatives or other body fluid of a patient where theantigen is circulating in the patient. Of course, it should beappreciated that the antigen may circulate in association with thepathogen, in association with components of the pathogen, in free form,or bound to a molecule or cell of the patient. Most preferably, theantigens are immunodominant and/or serodiagnostic antigens as presentedherein. For example, suitable tests include those in which one or morelabeled antibodies are used to detect presence of the antigen in bodilyfluid where the antigen may be captured (specifically or in bulk withother proteins) on a surface. There are numerous antigen detectionmethods known in the art and all of the known formats are deemedsuitable for use herein.

In certain embodiments, the diagnostic tools of the present inventioninvolve the recognition of the immunodominant antigens described hereinin an in vitro cellular assay determining the release of cytokines, suchas interferon gamma, from lymphocytes withdrawn from a subject currentlyor previously infected with a virulent mycobacterium.

With respect to suitable formulations of vaccines, it should berecognized that all known manners of producing such vaccines are deemedappropriate for use herein, and a person of ordinary skill in the artwill be readily able to produce such vaccines without undueexperimentation (see e.g., “Vaccine Adjuvants and Delivery Systems” byManmohan Singh; Wiley-Interscience (Jun. 29, 2007), ISBN: 0471739073; or“Vaccine Protocols” (Methods in Molecular Medicine) by Andrew Robinson,Martin P. Cranage, and Michael J. Hudson; Humana Press; 2 edition (Aug.27, 2003); ISBN: 1588291405). Therefore, suitable vaccines may beformulated as injectable solutions, or suspensions, intranasalformulations, transdermal or oral formulations.

The compositions, vaccines, diagnostic tests, etc., described herein maybe used for both human and veterinary use.

EXAMPLES

M. tuberculosis proteome microarray chip fabrication and probingmethods: Proteome microarrays were fabricated as described previously(Proc Natl Acad Sci USA 102(3): 547-552; Proteomics 7(10): 1678-1686;Proteomics 7(13): 2172-2183) with modifications. This and all otherextrinsic materials discussed herein are incorporated by reference intheir entirety. Where a definition or use of a term in an incorporatedreference is inconsistent or contrary to the definition of that termprovided herein, the definition of that term provided herein applies andthe definition of that term in the reference does not apply.

High-throughput construction of the M. tuberculosis ORFeome: Using theavailable M. tuberculosis sequence data primer pairs were designed forall ORFs encoded in the genome. Quality control was performed using gelelectrophoresis of PCR products. After three rounds of PCR, the finaltally was 97.3% successfully amplified. For cloning, PCR products weremixed with a linearized pXT7-based expression vector as describedpreviously and transformed into supercompetent DH5α cells. Thetransformed cells were cultured at 37° C. with vigorous aeration andwere checked for turbidity the following day. DNA was purified from theovernight cultures without prior colony selection using QIAprep 96 TurboMiniprep Kits from Qiagen. Of the 3998 successfully amplified PCRproducts, 3858 were cloned into the pXi vector (96.5% efficiency). Arandom sample of 1064 clones were tested by ‘QC-PCR’ in which using thesequence-specific primers were again used to verify that the clonedinserts were the expected size. Of these, 1007 were verified (94.6%)using this methodology.

More specifically, 4109 primer pairs were designed to amplify every ORFin the M. tuberculosis (strain H37Rv) genome annotated in Tuberculist(http://genolist.pasteur.fr/TubercuList/). Custom PCR primers comprising20 bp of gene-specific sequence with 33 bp of “adapter” sequences wereused in PCRs with genomic DNA as template. For genes >3 kb, additionalprimer pairs were designed to amplify overlapping fragments of 3 kbeach. All primer pairs used for this work are published at the UCIInstitute for Genomics and Bioinformatics (IGB) web portal athttp://contact14.ics.uci.edu/virus/tuber_index.php. The adaptersequences, which become incorporated into the termini flanking theamplified gene, are homologous to the cloning site of the linearized T7expression vector pXT7 and allow the PCR products to be cloned by invivo homologous recombination in competent DH5α cells. The resultingprotein incorporates an ATG translation start codon, a 5′ polyhistidineepitope, a 3′ influenza hemagglutinin epitope and a T7 terminator.

Array fabrication: Antibodies against the N-terminal poly-His and theC-terminal HA tags engineered into each protein were used to monitor theexpression in each spot. Positive and negative controls were built intoevery array and remaining spots on the array were in vitrotranscription/translation reactions expressing 4109 different M.tuberculosis clones representing the entire cloned ORFeome. Once RTSreactions were printed onto nitrocellulose and dried, no appreciabledegradation was observed after 6 months of storage in a desiccator at18° C. (data not shown). However, a reduction in signal and a reducedsignal-to-noise ratio associated with prolonged delay in printing afterthe end of the 5 h in vitro protein expression was observed. To minimizesuch reduction, in vitro expression reactions were staggered through theprint run. Thus, it is generally preferred that the reactions are nomore than 5, more preferably no more than 3, and most preferably no morethan 1 hour old before printing. Remaining variance in signals wasnormalized using positive and negative controls as described below.

Microarray chips were fabricated in batches of 50-100 2-pad slides(i.e., 100-200 arrays). Two standard deviations above the average of thenegative control intensity was used as a cut-off for detection of thetags. Overall, 3854 (96.4%) of the expressed proteins were positive forthe HIS tag, 3730 (93.3%) were positive for the HA tag, 3538 (91%) werepositive for both tags, and only 56 (1.4%) were negative for both tags,which means 98.6% of the expressed proteins were positive for at least 1of the tags.

In more detail, purified minipreps of DNA of 4109 clones (3998 fulllength ORFs plus 111 segments of ORFs>3 kb) were expressed in the E.coli based in vitro transcription/translation expression system fromRoche (RTS-100). 10 μl in vitro reactions were set up in sealed 384 wellplates and incubated for 5 h at 30° C. in a platform microshaker at 300RPM. A mixture of Tween-20 to a final concentration of 0.05% and aprotease inhibitor cocktail (Cømplete, Roche) were then added. Tominimize delay in printing after completion of protein expression, theinitiation of the RTS reactions was staggered. The RTS reactions wereprinted in singlicate without further purification onto 2-padnitrocellulose-coated FAST slides (Whatman) using an Omni Grid 100microarray printer (Genomic Solutions) in 4×4 sub-array format, witheach subarray comprising 17×17 spots. Each sub-array included 6 negativecontrol spots comprising ‘mock’ RTS reactions lacking DNA template. Eachsub-array also included positive control spots of 5 serial dilutions ofmouse, rat and human whole IgG. Together these positive and negativecontrols are used to normalize the data from different arrays (infra).Also included were 4 serial dilutions of purified recombinantEpstein-Barr virus nuclear antigen-1 (EBNA-1) which is recognized by themajority of humans and which serves as a useful guide to serum quality.Also printed were three recombinant M. tuberculosis proteins, 38 KDa(Rv0934), CFP-10 (Rv3874 (SEQ ID NO:547)), and ESAT-6 (Rv3875 (SEQ IDNO:548)). In addition, 6 serial dilutions of recombinant vascularendothelial growth factor (VEGF) from Invitrogen (Carlsbad Calif.) andtumor necrosis factor-α (TNF-α) were printed to be used as ahybridization controls by ‘spiking-in’ monoclonal anti-VEGF andanti-TNF-α antibodies into certain sera samples.

For probing with sera, the sera were diluted to 1/200 in Low CrossDilution Buffer (Candor Bioscience) containing E. coli lysate at a finalconcentration of 4-5 mg/ml protein, and incubated at room temperaturefor 30 minutes with constant mixing to block anti-E. coli antibodies.The arrays were rehydrated in blocking buffer (Candor Bioscience) for 30min and probed with the pretreated sera overnight at 4° C. with constantagitation. The slides were then washed 5× intris(hydroxymethyl)aminomethane (Tris)-buffered saline containing 0.05%(v/v) Tween 20, (T-TBS) and incubated in biotinylated anti-human IgG-Fc(Jackson Immuno Research) diluted 1/400 in dilution buffer. Afterwashing the slides three times each in T-TBS, bound antibodies werevisualized by incubation with streptavidin-conjugated SureLight® P-3(Columbia Biosciences). The slides were then washed three times each inT-TBS followed by TBS, and dipped in distilled water prior to air dryingby brief centrifugation. Protein expression was monitored on the printedarray by probing with monoclonal anti-polyhistidine (clone His-1, Sigma)and anti-hemagglutinin (clone 3F10, Roche) using biotinylated anti-mouseand anti-rat secondary antibodies, respectively followed bystreptavidin-conjugated SureLight® P-3.

Human sera: Sera were obtained from 927 patients enrolled from clinicalsites in several TB-endemic areas of the world using a cohort designthat included individuals presenting with respiratory symptomssuggestive of TB (TB suspects). Diagnosis of active TB was made on thebasis of evidence of growth of M. tuberculosis from sputum of patients(culture-confirmed active TB) (n=403). Diagnosis of non-TB disease wasmade on the basis of full microbiological and chest X ray (CXR)investigations (n=418). Non-TB disease cases included were those nottreated empirically for TB and who received adequate follow-up bysymptom screen, and CXR at times, to exclude TB. BCG vaccination statuswas not always known, but cohorts were all from countries that implementuniversal BCG vaccination at birth. For data analysis, active TB caseswere subdivided in smear positive TB (presence of M. tuberculosis insputum) and smear negative active TB. Cases in the TB and non-TB diseasegroup were also subdivided based on HIV comorbidity. Negative controlsera (n=42) were obtained from healthy, asymptomatic individuals from anon-endemic country (Italy) who were confirmed latent TB infection(LTBI)-negative by tuberculin skin test, Quantiferon assay andtuberculosis ELISPOT (T-spot) assay. The BCG vaccination status of thislatter set of donors is not known, but generally, individuals fromendemic countries are vaccinated and those from non-endemic countriesare not.

Data acquisition: Slides were scanned using a GenePix Autoloader 4200ALmicroarray confocal laser scanner (Molecular Devices) Median pixelintensity of the spots were quantified from tiff image files of probedarray scans using GenePix Pro 6.0 software (Molecular Devices).

Classification of immunoreactive antigens by proteomic features andfunction: Antigens were classified according to the FunctionalClassification Codes annotated on TubercuList, Computational predictionswere also made using SignalP (J Mol Biol 340(4): 783-795) and PSORTb(Bioinformatics 21(5): 617-623) (http://db.psort.org) to predict thepresence probability of signal peptides and cellular localization,respectively.

Screening the proteome for serodiagnostic antigens: Representativearrays probed with serum from each group are shown in FIGS. 1A and 1B.Here, panel (A) shows culture-confirmed TB-positive individual, andpanel (B) shows latent TB infected-negative control individual. Eacharray contained positive and negative control spots. The IgG controlspots, which control for secondary antibody, were positive in botharrays. Neither individuals reacted with the negative (‘no DNA’) controlreactions. Both groups of individuals reacted to EBNA-1, indicatingprior exposure to EBV, and the group of acute infected individuals, hada robust antibody response to several M. tuberculosis antigens.

One evaluation of the array was performed by calculating a cut-off valueabove the mean+2 SD of the control (‘no DNA’) signals. By this criterionit was noted that sera from both TB-positive and control individualsreacted to antigens on the array. Even by visual estimation, however, itwas evident that TB-confirmed patients reacted more intensely andagainst more antigens than the controls. To determine whether thesignals seen for M. tuberculosis antigens were E. coli-specificantibodies against which blocking had failed, E. coli lysateconcentration was increased. However, this had no effect on thesesignals (data not shown). Lysate prepared from M. tuberculosis was alsoincluded with the result that this completely abolished all signals onthe array (data not shown), which indicates that the signals seen on thearray are due to M. tuberculosis-specific antibodies in the sera.

Protein Microarray Data Analysis:

Microarray data were analyzed by four methods, summarized below. Log10-transformed data were used for first three methods and VSN-normalizeddata were used for the fourth method. FIG. 4A shows proteins ranking <10in at least one of three analytical methods (random forests, CERNO, andrandom forests with CERNO-prefiltered data) in a comparison between TBcases (n=400) and non-TB disease cases (n=418). Relative ranks ofproteins (max rank ˜4000) in each method are shown. N/A, not available;this implies that the protein was pre-filtered by CERNO (p value forfiltration >0.005). FIG. 4B shows the same as FIG. 4A, but for acomparison between TB cases (n=255) and non-TB disease cases (n=307)among HIV negative persons only.

1. TB and non-TB samples were classified by Random Forests, aclassification method based on multiple classification trees. Randomforests queries (comparisons of TB to non-TB disease classes) wereperformed with data collected from sera from endemic countries, and withdata stratified for HIV status and for smear status of TB patients.Antigens were ranked from most informative to least informative based onmean decrease accuracy output of a particular query (highest meandecrease accuracy corresponds to highest rank). The random forestsanalysis was conducted with and without a pre-filtering step using theCERNO statistical calculation.

2. CERNO p-values provide an association of high relative intensitieswith active tuberculosis diagnosis. Antigens were ranked by decreasingp-value.

3. The data were also analyzed to identify antigens that exhibitunusually high binding in TB samples relative to the non-TB diseasesamples by the following, sequential calculations: (i) the mean andvariance for each antigen in non-TB from endemic areas; (ii) a Z score(number of standard deviations from the mean for an antigen in thenon-TB disease class) for each antigen in each sample in one comparison(TB vs non-TB disease from endemic countries); (iii) a p-valuecorresponding to the Z score (expected normal distribution tail areaabove the value); (iv) the adjusted p-values (Benjamini-Hochberg) foreach profile; (v) reactivity vs no reactivity at the p-adjusted level of0.01 (false discovery rate of one percent). Antigens were ranked bynumber of reactivity calls in the TB group.

4. To stabilize variance of the raw data, a variant of thelog-transformation (a sin h) was used (Bioinformatics 20(5): 660-667),and negative and positive control spots (the ‘no DNA’ and IgG spots,respectively) were used to normalize the data using the “VSN” package inR from the Bioconductor suite (http://Bioconductor.org/). A p-value onthe normalized data was prepared by comparing signals between theconfirmed TB-positive and LTBI-negative control groups using aBayes-regularized t-test adapted from Cyber-T for use with proteinarrays (Bioinformatics 17(6): 509-519; J Biol Chem 276(23): 19937-19944;Bioinformatics 22(14): 1760-1766; Bioinformatics 23(13): i508-518). Toaccount for multiple test conditions, Benjamini Hochberg p-valueadjustments were calculated. Reactive antigens were defined asserodiagnostic or cross-reactive by having a Benjamini Hochbergcorrected p-value <0.05 or >0.05, respectively, and an average signalintensity >2 std. dev above the mean of the negative control (no DNA)spots on the smear positive samples. Multiple antigen classifiers werebuilt using Support Vector Machines (SVMs). The “e1071” and “ROCR”packages in R were utilized to train the SVMs and to produce receiveroperating characteristic (ROC) curves, respectively. For other graphicrepresentations such as heat maps and histograms, normalized data wereretransformed into approximate raw values.

With the methods above, a total of 250 antigens were selected bycombining top 50 ranks from Random Forests (RF) and CERNO for queries onall TB and non-TB disease patients, all HIV negative TB and non-TBdisease patients (with and without stratification by smear), plus top 10ranks for HIV-positive TB and non-TB disease query, plus reactivitycalls of >3 in TB category, plus Benjamini Hochberg adjusted Cyber T pvalue <0.05. Seven sets of antigens were prioritized based on agreementby the methods, with the antigens of the first set being the mostpreferred.

The most preferred sequences encoding the antigens were characterized byRF or CERNO (p<0.005) plus reactivity calls, RF (<10) and CERNO(p<0.005), and Benjamini Hochberg adjusted Cyber T p value <0.05:Rv0798c (SEQ ID NO: 121), Rv1886c (SEQ ID NO:270), Rv2031c (SEQ IDNO:284), Rv3616c (SEQ ID NO:509), Rv3804c (SEQ ID NO:534), Rv3874 (SEQID NO:547).

The following sequences producing the antigens were determined to besecond most preferential, characterized by RF or CERNO (p<0.005) plusreactivity calls, RF (<10) and CERNO (p<0.005): Rv0302 (SEQ ID NO:52),Rv0379 (SEQ ID NO:65), Rv0394c (SEQ ID NO:66), Rv0456c (SEQ ID NO:74),Rv0632c (SEQ ID NO:103), Rv0944 (SEQ ID NO:142), Rv0984 (SEQ ID NO:146),Rv1030 (SEQ ID NO:153), Rv1196 (SEQ ID NO:174), Rv1242 (SEQ ID NO:180),Rv1284 (SEQ ID NO:187), Rv1387 (SEQ ID NO:206), Rv1837c (SEQ ID NO:264),Rv1926c (SEQ ID NO:275), Rv1980c (SEQ ID NO:281), Rv2094c (SEQ IDNO:294), Rv2544 (SEQ ID NO:363), Rv2618 (SEQ ID NO:375), Rv2746c (SEQ IDNO:391), Rv2870c (SEQ ID NO:407), Rv2873 (SEQ ID NO:408), Rv2875 (SEQ IDNO:409), Rv3050c (SEQ ID NO:434), Rv3248c (SEQ ID NO:458), Rv3376 (SEQID NO:478), Rv3763 (SEQ ID NO:527), Rv3810 (SEQ ID NO:536), Rv3864 (SEQID NO:545).

The following sequences producing the antigens were determined to bethird most preferential, characterized by Benjamini Hochberg adjustedCyber T p value <0.05: Rv2252 (SEQ ID NO:323), Rv2282c (SEQ ID NO:569),Rv0212c (SEQ ID NO:557), Rv3243c (SEQ ID NO:456), Rv3675 (SEQ IDNO:519), Rv2984 (SEQ ID NO:423), Rv1175c (SEQ ID NO:169), Rv3326 (SEQ IDNO:578), Rv3628 (SEQ ID NO:513), Rv3775 (SEQ ID NO:584), Rv3362c (SEQ IDNO:475), Rv0801 (SEQ ID NO:122), Rv1629 (SEQ ID NO:566), Rv0272c (SEQ IDNO:558), Rv3762c (SEQ ID NO:583), Rv3319 (SEQ ID NO:577), Rv3495c (SEQID NO:581), Rv2151c (SEQ ID NO:308).

The following sequences producing the antigens were determined to befourth most preferential, characterized by reactivity calls: Rv0227c(SEQ ID NO:37), Rv0280 (SEQ ID NO:50), Rv0993 (SEQ ID NO:148), Rv1306(SEQ ID NO:192), Rv1363c (SEQ ID NO:204), Rv2050 (SEQ ID NO:288), Rv2116(SEQ ID NO:299), Rv3417c (SEQ ID NO:486), Rv3653 (SEQ ID NO:516).

The following sequences producing the antigens were determined to befifth most preferential, characterized by ranks <10 by either CERNO orRF: Rv1253 (SEQ ID NO:182), Rv3413c (SEQ ID NO:485), Rv1635c (SEQ IDNO:232), Rv3021c (SEQ ID NO:432), Rv1193 (SEQ ID NO:173), Rv2592c (SEQID NO:369), Rv3620c (SEQ ID NO:510), Rv0929 (SEQ ID NO:139), Rv0959 (SEQID NO:145), Rv1162 (SEQ ID NO:166), Rv2389c (SEQ ID NO:341), Rv2984 (SEQID NO:423), Rv2588c (SEQ ID NO:367), Rv0171 (SEQ ID NO:26), Rv1865c (SEQID NO:267), Rv2074 (SEQ ID NO:290).

The following sequences producing the antigens were determined to besixth most preferential, characterized by ranks <25 by either CERNO orRF: Rv0543c (SEQ ID NO:87), Rv1677 (SEQ ID NO:237), Rv1304 (SEQ IDNO:191), Rv2841c (SEQ ID NO:400), Rv3680 (SEQ ID NO:520), Rv0831c (SEQID NO:125), Rv2032 (SEQ ID NO:285), Rv3127 (SEQ ID NO:446), Rv3272 (SEQID NO:464), Rv3323c (SEQ ID NO:470), Rv3508 (SEQ ID NO:494), Rv3628 (SEQID NO:513), Rv1173 (SEQ ID NO:167), Rv2623 (SEQ ID NO:376), Rv0527 (SEQID NO:85), Rv1620c (SEQ ID NO:229), Rv1901 (SEQ ID NO:272), Rv2151c (SEQID NO:308), Rv0362 (SEQ ID NO:60), Rv3129 (SEQ ID NO:447), Rv3140 (SEQID NO:449), Rv0340 (SEQ ID NO:56), Rv2792c (SEQ ID NO:395), Rv3003c (SEQID NO:426), Rv3019c (SEQ ID NO:431), Rv3862c (SEQ ID NO:544), Rv0572c(SEQ ID NO:91), Rv2477c (SEQ ID NO:356), Rv2659c (SEQ ID NO:379), Rv0311(SEQ ID NO:54), Rv0350 (SEQ ID NO:57), Rv2127 (SEQ ID NO:301), Rv3875(SEQ ID NO:548), Rv0877 (SEQ ID NO:134), Rv1916 (SEQ ID NO:274), Rv2138(SEQ ID NO:303), Rv2847c (SEQ ID NO:403), Rv3118 (SEQ ID NO:444),Rv2495c (SEQ ID NO:358), Rv3669 (SEQ ID NO:517), Rv0281 (SEQ ID NO:51),Rv2711 (SEQ ID NO:383), Rv2744c (SEQ ID NO:390), Rv3803c (SEQ IDNO:533), Rv1239c (SEQ ID NO:179), Rv2147c (SEQ ID NO:307), Rv2253 (SEQID NO:324), Rv0308 (SEQ ID NO:53), Rv0587 (SEQ ID NO:95), Rv1564c (SEQID NO:224), Rv2185c (SEQ ID NO:313).

The following sequences producing the antigens were determined to beseventh most preferential, characterized by ranks between 26 and 50 byeither CERNO or RF: Rv1805c (SEQ ID NO:261), Rv2729c (SEQ ID NO:386),Rv3386 (SEQ ID NO:481), Rv3515c (SEQ ID NO:497), Rv0772 (SEQ ID NO:116),Rv2948c (SEQ ID NO:420), Rv0006 (SEQ ID NO:1), Rv1906c (SEQ ID NO:273),Rv2244 (SEQ ID NO:322), Rv2468c (SEQ ID NO:354), Rv3701c (SEQ IDNO:522), Rv0054 (SEQ ID NO:6), Rv1945 (SEQ ID NO:277), Rv3345c (SEQ IDNO:472), Rv0276 (SEQ ID NO:48), Rv0709 (SEQ ID NO:108), Rv1527c (SEQ IDNO:220), Rv2048c (SEQ ID NO:287), Rv2414c (SEQ ID NO:345), Rv3524 (SEQID NO:499), Rv3556c (SEQ ID NO:502), Rv1322 (SEQ ID NO:196), Rv2934 (SEQID NO:417), Rv0270 (SEQ ID NO:47), Rv0612 (SEQ ID NO:99), Rv1699 (SEQ IDNO:242), Rv2728c (SEQ ID NO:385), Rv3017c (SEQ ID NO:430), Rv3364c (SEQID NO:476), Rv3418c (SEQ ID NO:487), Rv3718c (SEQ ID NO:525), Rv0426c(SEQ ID NO:70), Rv1181 (SEQ ID NO:171), Rv1725c (SEQ ID NO:250), Rv0256c(SEQ ID NO:44), Rv0605 (SEQ ID NO:98), Rv0737 (SEQ ID NO:114), Rv0834c(SEQ ID NO:126), Rv1255c (SEQ ID NO:184), Rv2224c (SEQ ID NO:320),Rv1843c (SEQ ID NO:265), Rv2333c (SEQ ID NO:334), Rv2490c (SEQ IDNO:357), Rv3183 (SEQ ID NO:454), Rv0668 (SEQ ID NO:106), Rv1556 (SEQ IDNO:223), Rv1673c (SEQ ID NO:236), Rv3513c (SEQ ID NO:496), Rv3675 (SEQID NO:519), Rv3870 (SEQ ID NO:546), Rv3891c (SEQ ID NO:552), Rv0163 (SEQID NO:24), Rv0710 (SEQ ID NO:109), Rv1297 (SEQ ID NO:189), Rv1745c (SEQID NO:255), Rv0600c (SEQ ID NO:97), Rv1536 (SEQ ID NO:222), Rv1738 (SEQID NO:254), Rv2524c (SEQ ID NO:359), Rv3086 (SEQ ID NO:440), Rv3367 (SEQID NO:477), 1670135c (SEQ ID NO:20), Rv0627 (SEQ ID NO:101), Rv1448c(SEQ ID NO:213), Rv3224a (SEQ ID NO:455), Rv0029 (SEQ ID NO:2), 1670846c(SEQ ID NO:129), Rv1159 (SEQ ID NO:165), Rv1186c (SEQ ID NO:172),Rv1705c (SEQ ID NO:243), Rv1713 (SEQ ID NO:248), Rv2476c (SEQ IDNO:355), Rv3402c (SEQ ID NO:483), Rv2615c (SEQ ID NO:374), Rv2995c (SEQID NO:425), Rv3788 (SEQ ID NO:585), Rv0140 (SEQ ID NO:555), Rv0203 (SEQID NO:33), Rv1531 (SEQ ID NO:565), Rv1693 (SEQ ID NO:241), Rv1882c (SEQID NO:269), Rv2143 (SEQ ID NO:568), Rv2367c (SEQ ID NO:570), Rv0584 (SEQID NO:94), Rv1651c (SEQ ID NO:567), Rv3197a (SEQ ID NO:576), Rv3369 (SEQID NO:579), Rv3825c (SEQ ID NO:586), Rv0101 (SEQ ID NO:15), Rv0808 (SEQID NO:123), Rv0814c (SEQ ID NO:560), Rv2153c (SEQ ID NO:309), Rv2933(SEQ ID NO:416), Rv0071 (SEQ ID NO:9), Rv2471 (SEQ ID NO:571), Rv2979c(SEQ ID NO:575), Rv0155 (SEQ ID NO:556), Rv0581 (SEQ ID NO:559), Rv2631(SEQ ID NO:377), Rv3455c (SEQ ID NO:489), Rv3601c (SEQ ID NO:505),Rv0896 (SEQ ID NO:562), Rv1641 (SEQ ID NO:234), Rv3005c (SEQ ID NO:427),Rv3759c (SEQ ID NO:582), Rv3800c (SEQ ID NO:532), Rv0187 (SEQ ID NO:30),Rv2379c (SEQ ID NO:338), Rv2434c (SEQ ID NO:352), Rv2940c (SEQ IDNO:574), Rv3477 (SEQ ID NO:580), Rv0435c (SEQ ID NO:72), Rv0844c (SEQ IDNO:128), Rv0856 (SEQ ID NO:561), Rv1191 (SEQ ID NO:564), Rv2803 (SEQ IDNO:397), Rv0783c (SEQ ID NO:118), Rv1054 (SEQ ID NO:563), Rv1689 (SEQ IDNO:240), Rv2539c (SEQ ID NO:572), Rv2859c (SEQ ID NO:573), Rv3777 (SEQID NO:528).

In additional methods, to identify serodiagnostic antigens, t-tests foreach reactive antigen were performed comparing normalized signalintensities of TB-cases to controls, and exemplary results are shown inFIG. 2A. Here, Cyber T-tests revealed signals for 23 antigens assignificantly different between the smear-positive TB cases (n=13) andthe LTBI-negative controls (n=69). These antigens are shown in thehistogram by the average of their normalized signal intensities for thetwo patient groups, and ranked in descending order of the signals in thesmear-positive group. The p-value for each antigen is also shown (top),arranged so that the more significant antigens produce downward pointingspikes.

Based on probing sera from 48 LTBI-negative subjects and 50 TB culturepositive subjects, a total of 31 antigens were found to discriminatebetween these groups and were considered serodiagnostic as depicted inFIG. 2B. It was further found that combining multiple antigens producesa test with increased specificity and sensitivity. The top 2discriminatory antigens have an AUC of >0.88, and the addition ofanother 3 antigens to the classifier improves the AUC score to >0.90.Using 10 antigens gives an AUC score of >0.93. Remarkably, furtheraddition of antigens does not improve the AUC score of the classifier.For the sera in this study the top 10 discriminatory antigens yields asensitivity of >80% identification of true negatives and a sensitivityof >90% for finding the true positives. These results clearly supportthe ability of whole proteome chips using ORFeomes created usingenzymeless recombination cloning, and proteomes expressed using E. colibased cell free expression systems, as valid tools for serodiagnosticantigen discovery. These classifiers will benefit from a larger, morecomprehensive profiling study of well characterized serum samples.

The inventors then studied the diagnostic power of different numbers ofORFs using receiver operating characteristic (ROC) curves. A ROC curveis a parametric plot of the false positive rate (1—specificity) vs. thetrue positive rate (sensitivity) of a classifier as the underlyingdiscrimination threshold is varied. The area under the curve (AUC)summarizes the results. An AUC of 1.0 indicates a perfect classifier,while an AUC of 0.51 (95% confidence interval, 0.43 to 0.59) is theexpected value for a classifier that works by chance for the data set,as inferred by the method of Truchon and Bayly (J Chem Inf Model 47(2):488-508). For multiple antigens, kernel methods and support vectormachines were used (Bioinformatics: the Machine Learning Approach,Second Edition edn.: MIT Press) to build linear and nonlinearclassifiers. As input to the classifier, the highest-ranking 1, 2, 5,10, and 30, ORFs were used on the basis of either p-value or singleantigen AUC and the results were validated with 10 runs of threefoldcross-validation. The results (data not shown) showed that increasingthe antigen number from 1 to 5, and from 5 to 10 produced an incrementalimprovement in the classifier. Increasing numbers beyond this did notimprove the algorithm's ability to discriminate the two populations.Contingency tables built on these data showed that using 10 antigens atan optimal threshold provides an accuracy of 94% of the true positivesand 78% of the true negatives.

Alternatively, antigen selection was also performed as follows: Raw datawere distributed into the two groups of the query and subsets werenormalized using vsn on the control spots. A CyberT test was run on thenormalized data, and SVM classifier was built with a subset of the topantigens. Duplicates were removed. Each sample included meta data thatwas used to build each of the 10 queries, and each group was a disjointsubset of the original data, and each query only had two groups. Datawere normalized using ar sin h normalization (Bioinformatics, 18 Suppl1, 2002), which compensates for variance dependence on mean. Anaffine-linear transformation (scale all value+add a value) was performedon each sample to compensate for shifts between samples, thus allowing at-test on the normalized data. The CyberT test was used to estimate thevariance of a spot by using neighboring spots (Bioinformatics,17(6):509-519, 2001), giving a statistical measure of the difference inmeans between two groups for a particular antigen. Subsetting thep-values: Antigens are subset based on the significance of the p-value.Multiple test correction is used, and antigens are subset on theBonferroni or the Benjamini-Hochberg p-value (<0.05) in most cases.Building a (SVM) classifier: Classifiers were built using a number ofthe top antigens to provide an estimate of what classification accuracywe could be obtained for each query. This allows for determination ofthe optimal number of antigens to be included in the final classifier.3-fold cross-validation was used and ROC plots were generated tovisualize the results. A list of exemplary results using this analysisis provided in the list of serodiagnostic antigens shown in FIG. 2C.

Enrichment analysis: To determine the features of proteins that wereenriched in the immunodominant antigen set, proteins were classifiedinto one of 11 functional categories according to the TubercuList genomedatabase (http://genolist.pasteur.fr/TubercuList/). The number of ‘hits’for each category was determined in the immunodominant antigen set. 7immunodominant antigens were considered serodiagnostic, of which 4(57.1%) were proteins with proline-glutamic (PE/PPE) motifs. Since thewhole proteome contains 168 (4.2%) PE/PPE motif proteins, thisrepresents a significant 13.6-fold enrichment relative to the wholeproteome. Importantly, none of the 167 ‘cross-reactive’ immunodominantantigens were significantly enriched in any of the functionalcategories. The number of serodiagnostic antigens could be increased to31 if all antigens were assessed regardless of immunodominance. Ofthese, 6 (19.4%) were virulence factors and 10 (32.2%) were PE/PPE motifproteins, representing a significant 7.7-fold enrichment for both,relative to the whole proteome. Interestingly, molecules involved inintermediary metabolism were significantly underrepresented (0.1-foldenrichment) in the serodiagnostic set relative to the whole proteome.

Several computational predictions were also made to classify theantigens. Lipoproteins and cell wall proteins were not enriched in theserodiagnostic antigen set, whereas possession of a signal sequence oran extracellular classification by PSORTb were enriching. High coilcontent, high glycine and high proline were all enriching features.PE/PPE molecules, characterized as having highly conserved proline richmotifs 100-200 amino acids long with high coil content near theN-terminus, were significant enriching features. Twenty-six out of 31molecules in the serodiagnostic antigen set were negatively charged withisoelectric point <6.7. Again, none of these predicted features wereenriched in the cross reactive antigen set.

Comparison of fluorescence and colorimetric detection of boundantibodies: The ability to replace fluorescence detection with acolorimetric methodology would assist in wider deployment of the arrayswhere fluorescence scanners would be impractical or where a smallerdevice would be preferable, such as in high containment laboratories orroutine diagnostic laboratories. However, it was not known whether acolorimetric readout would have a reduced sensitivity or dynamic rangecompared to fluorescence. With this aim the HIS and HA tag-specificmonoclonal antibodies were visualized with appropriate alkalinephosphatase-conjugated secondary antibodies and the arrays weredeveloped with nitro-TB developer. Grey scale 2400 dpi resolution TIFFimages were obtained using a conventional desktop document scanner andscatter plots of the 4608 data points compared with fluorescentdetection. The correlation for signals for the HIS and HA tags were high(r2=0.8186 and 0.9259, respectively). Fluorescence based detection gave99.2%, 97.0%, 96.6% and 0.4% for poly-His tag detection, HA tagdetection, both tag detection and no tag detection, respectively.Colorimetric based detection gave 93.7%, 88.6%, 84.8% and 2.5% forpoly-His tag detection, HA tag detection, both tag detection and no tagdetection respectively. While fluorescence based detection is somewhatmore sensitive (since there were fewer ‘double negatives’), alkalinephosphatase based detection is a comparable alternative that can beperformed with only basic equipment. FIG. 3 depicts representative scansof arrays proved with antibodies to (A) HIS and (B) HA tag antibodiesand visualized by fluorescence and colorimetric means; scatter plots areof colorimetric vs. fluorescence data.

Further illustrative exemplary methods and protocols are provided in theparent application PCT/US07/23299 (published as WO2008/140478), which isincorporated by reference herein.

Thus, specific embodiments and applications of compositions and methodsrelated to antigens of M. tuberculosis have been disclosed. It should beapparent, however, to those skilled in the art that many moremodifications besides those already described are possible withoutdeparting from the inventive concepts herein. The inventive subjectmatter, therefore, is not to be restricted except in the spirit of theappended claims. Moreover, in interpreting both the specification andthe claims, all terms should be interpreted in the broadest possiblemanner consistent with the context. In particular, the terms “comprises”and “comprising” should be interpreted as referring to elements,components, or steps in a non-exclusive manner, indicating that thereferenced elements, components, or steps may be present, or utilized,or combined with other elements, components, or steps that are notexpressly referenced. Furthermore, where a definition or use of a termin a reference, which is incorporated by reference herein isinconsistent or contrary to the definition of that term provided herein,the definition of that term provided herein applies and the definitionof that term in the reference does not apply.

Sequence Listing

The Sequence Listing providing sequences with the SEQ ID NO:1 to SEQ IDNO:586 is submitted as a single file in computer readable format,wherein the single file is entitled“101519.0003US4_SequenceListing_ST25.txt”, which was created Jul. 9,2012, which has a size of 950 kb, and which is incorporated by referenceherein.

What is claimed is:
 1. A method for the detecting presence of antibodieswhich specifically bind to antigens of M. tuberculosis and which arepresent in a bodily fluid sample, comprising contacting the sample withantigens of M. tuberculosis, wherein the antigens are encoded by atleast two of nucleic acids Rv1886c (SEQ ID NO: 270), Rv1860 (SEQ ID NO:588), Rv3874 (SEQ ID NO: 547), Rv0798c (SEQ ID NO: 121), Rv3804 (SEQ IDNO:534), Rv2031 (SEQ ID NO: 284), Rv0934 (SEQ ID NO: 587), and Rv0379(SEQ ID NO:65), and detecting antibodies which bind to the antigens. 2.The method of claim 1, wherein the antigens of M. tuberculosis arepresent in a crude expression extract or in partially purified form. 3.The method of claim 1, wherein the step of detecting the antibodiescomprises use of a signal-generating anti-antibody.
 4. The method ofclaim 1, wherein binding affinity of respective antibodies whichspecifically bind to antigens of M. tuberculosis are known andindicative of an activity state of tuberculosis.
 5. The method of claim1, wherein the antigens of M. tuberculosis are coupled to a solid phaseprior to the step of contacting the sample with the antigens.
 6. Themethod of claim 5, wherein the antigens of M. tuberculosis are coupledto the solid phase in an array.
 7. The method of claim 6, wherein atleast one of the antigens encoded by at least two of nucleic acidsRv1886c (SEQ ID NO: 270), Rv1860 (SEQ ID NO: 588), Rv3874 (SEQ ID NO:547), Rv0798c (SEQ ID NO: 121), Rv3804 (SEQ ID NO: 534), Rv2031 (SEQ IDNO: 284), Rv0934 (SEQ ID NO: 587), and Rv0379 (SEQ ID NO: 65) is presentas an antibody-binding fragment.
 8. The method of claim 6, wherein theantigens of M. tuberculosis further comprise at least one antigen of M.tuberculosis that is encoded by a sequence selected from the groupconsisting of SEQ ID NO:1 to SEQ ID NO:589, or antibody bindingfragments thereof.
 9. A method for the detecting presence of antibodieswhich specifically bind to antigens of M. tuberculosis and which arepresent in a bodily fluid sample, comprising contacting the sample withantigens of M. tuberculosis, wherein the antigens are encoded by atleast one nucleic acid selected from the group consisting of Rv1886c(SEQ ID NO: 270), Rv1860 (SEQ ID NO: 588), Rv3874 (SEQ ID NO: 547),Rv0798c (SEQ ID NO: 121), Rv3804 (SEQ ID NO: 534), Rv2031 (SEQ ID NO:284), Rv0934 (SEQ ID NO: 587), Rv0379 (SEQ ID NO: 65), and at least oneof Rv3864 (SEQ ID N0:545), Rv1980 (SEQ ID NO:281), Rv0632 (SEQ IDNO:103), Rv3810 (SEQ ID NO:536), Rv1837 (SEQ ID NO:264), Rv1196 (SEQ IDNO:1 74), Rv3248 (SEQ ID NO:458), Rv3628 (SEQ ID NO:513), Rv1284 (SEQ IDNO:187), Rv1411c (SEQ ID NO: 589), Rv3616c (SEQ ID NO:509), and Rv0456c(SEQ ID NO:74), and detecting antibodies which bind to the antigens. 10.The method of claim 9, wherein the step of contacting the sample isperformed with two or more antigens of M. tuberculosis.
 11. The methodof claim 9, wherein the antigens of M. tuberculosis further comprise atleast one antigen of M. tuberculosis that is encoded by at least twosequences selected from the group consisting of SEQ ID NO:1 to SEQ IDNO:589, or antibody binding fragments thereof.
 12. A diagnostic devicefor detection presence of antibodies which specifically bind to antigensof M. tuberculosis and which are present in a bodily fluid sample,comprising a solid phase to which antigens are coupled, wherein theantigens are encoded by at least two of nucleic acids selected from thegroup consisting of Rv1886c (SEQ ID NO: 270), Rv1860 (SEQ ID NO: 588),Rv3874 (SEQ ID NO: 547), Rv0798c (SEQ ID NO: 121), Rv3804 (SEQ ID NO:534), Rv2031 (SEQ ID NO: 284), Rv0934 (SEQ ID NO: 587), Rv0379 (SEQ IDNO: 65), and optionally at least one of Rv3864 (SEQ ID N0:545), Rv1980(SEQ ID NO:281), Rv0632 (SEQ ID NO:103), Rv3810 (SEQ ID NO:536), Rv1837(SEQ ID NO:264), Rv1196 (SEQ ID NO: 174), Rv3248 (SEQ ID NO:458), Rv3628(SEQ ID NO:513), Rv1284 (SEQ ID NO:187), Rv1411c (SEQ ID NO:589),Rv3616c (SEQ ID NO:509), and Rv0456c (SEQ ID NO:74), and wherein thedevice is suitable for detection of the presence of the antibodiesaccording to claim
 1. 13. The diagnostic device of claim 12, whereinbinding of the antibodies is indicative of active tuberculosis.